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Related Experiment Video

Updated: May 20, 2025

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028
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Structural study on human microbiome-derived polyketide synthases that assemble genotoxic colibactin.

Minjae Kim1, Jinwoo Kim1, Gyu Sung Lee2

  • 1Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.

Structure (London, England : 1993)
|May 17, 2025
PubMed
Summary

Researchers uncovered the structures of key enzymes in colibactin (a gut toxin promoting cancer) biosynthesis. This reveals how these enzymes interact, advancing understanding of this cancer-promoting genotoxin and its NRPS-PKS pathway.

Keywords:
NRPSPKSacyl carrier proteinacyltransferasecolibactincryo-electron microscopyketosynthasemicrobiomenatural product

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Microbiology

Background:

  • Colibactin is a genotoxin from the human microbiome that drives colorectal cancer by damaging host gut epithelial DNA.
  • Colibactin biosynthesis involves a hybrid non-ribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) pathway, but enzyme structures are poorly understood.

Purpose of the Study:

  • To determine the cryo-electron microscopy (cryo-EM) structures of two critical colibactin-producing polyketide synthase (PKS) enzymes, ClbC and ClbI.
  • To elucidate the structural basis of enzyme-substrate interactions and inter-enzyme complex formation within the colibactin assembly line.

Main Methods:

  • Utilized cryo-electron microscopy (cryo-EM) to capture high-resolution structures of ClbC and ClbI.
  • Employed a substrate-mimic crosslinker to trap enzymes in distinct functional states.
  • Analyzed protein-protein interactions between NRPS and PKS enzymes.

Main Results:

  • Determined the structures of ClbC and ClbI, revealing carrier protein (CP) domain binding sites on ketosynthase (KS) domains.
  • Identified a novel docking interaction between ClbI and its upstream enzyme ClbH.
  • Established a 1:2 stoichiometry for the ClbH-ClbI complex, mediated by ClbH's C-terminal peptide and ClbI's dimeric interface.

Conclusions:

  • The structural insights advance the understanding of the colibactin biosynthetic machinery.
  • Findings provide a foundation for future studies on NRPS-PKS pathway mechanisms and potential therapeutic targeting of colibactin production.